Contacts of the helix formed by residues 385 - 396 (chain A) in PDB entry 4X5O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A SER 5.6 0.4 - - - -
357A VAL* 2.7 25.6 + - - +
358A ALA* 4.2 1.2 - - - +
383A SER 4.2 0.2 - - - -
384A ILE* 1.3 65.4 - - - +
386A VAL* 1.3 64.2 + - - -
387A GLU* 3.1 4.0 - - - -
388A ARG* 3.0 15.8 + - - +
389A ILE* 3.0 26.3 + - - +
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 5.2 0.9 - - + -
77A PHE* 3.9 12.6 - - + -
80A ILE* 3.6 30.5 - - + -
172A TYR* 3.7 39.3 - - + +
174A CYS* 3.7 18.6 - - + -
384A ILE* 2.6 23.3 + - + +
385A GLY* 1.3 71.4 - - - -
387A GLU* 1.3 59.4 + - - +
389A ILE* 3.7 8.6 - - - -
390A PHE* 2.8 50.1 + - + -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.0 24.8 + - - -
65A TYR* 3.1 18.6 + - - -
166A GLY 5.9 2.7 - - - +
168A TYR* 5.1 4.5 - - - -
171A PHE* 3.6 21.5 - - + -
172A TYR* 3.0 44.2 + - + +
385A GLY 3.1 1.1 - - - -
386A VAL* 1.3 80.1 - - - +
388A ARG* 1.3 62.0 + - + +
390A PHE* 3.6 15.1 - - - +
391A SER* 3.6 18.4 + - - -
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY* 6.0 4.6 - - - -
355A GLY* 5.8 2.5 - - - -
356A SER* 2.5 57.2 + - - +
357A VAL* 5.2 7.2 - - + -
385A GLY* 3.0 14.5 + - - +
387A GLU* 1.3 79.1 - - + +
389A ILE* 1.3 64.4 + - + +
391A SER* 3.3 8.7 + - - -
392A ILE* 3.2 30.1 + - + +
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Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 4.1 13.5 - - + -
80A ILE* 5.2 1.8 - - + -
199A LEU* 4.3 6.7 - - + -
202A LEU* 3.7 34.3 - - + -
204A ILE* 4.3 12.6 - - + -
357A VAL* 3.6 26.7 - - + -
384A ILE* 3.6 31.0 - - + -
385A GLY 3.0 12.5 + - - +
386A VAL* 3.8 6.5 - - - +
388A ARG* 1.3 73.2 - - - +
390A PHE* 1.3 64.3 + - - +
392A ILE* 3.3 7.5 + - - +
393A VAL* 3.1 33.6 + - + +
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Residues in contact with PHE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 5.4 4.7 - - - +
65A TYR* 4.7 9.2 - + - -
72A VAL* 3.9 8.6 - - + +
73A ARG* 3.7 41.1 - - + -
76A VAL* 3.7 31.9 - - + -
77A PHE* 3.7 26.9 - + - -
172A TYR* 4.2 20.0 - + - -
386A VAL* 2.8 36.4 + - + +
387A GLU* 3.6 22.7 - - - +
389A ILE* 1.3 77.8 - - - +
391A SER* 1.3 62.3 + - - +
393A VAL* 3.3 3.4 + - - +
394A GLU* 3.2 30.4 + - - +
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Residues in contact with SER 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A GLU 3.6 7.9 + - - -
388A ARG* 3.3 10.4 + - - -
390A PHE* 1.3 79.6 - - - +
392A ILE* 1.3 64.3 + - - +
394A GLU* 3.3 15.9 + - - +
395A GLN* 3.2 38.8 + - - +
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 4.3 30.3 - - + +
340A LEU* 3.5 29.6 - - + -
357A VAL* 5.5 5.2 - - + -
388A ARG* 3.2 22.6 + - + +
389A ILE* 3.7 9.9 - - - +
390A PHE 3.3 0.2 - - - -
391A SER* 1.3 79.2 - - - +
393A VAL* 1.3 58.8 + - - +
395A GLN* 3.5 4.9 + - - +
396A ARG* 3.0 42.6 + - + +
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 3.8 26.5 - - + +
75A LYS* 6.3 2.5 - - + -
76A VAL* 4.0 19.7 - - + -
202A LEU* 5.1 5.6 - - + +
204A ILE* 4.1 22.9 - - + -
389A ILE* 3.1 21.3 + - + +
390A PHE 3.8 3.6 - - - +
392A ILE* 1.3 78.2 - - - +
394A GLU* 1.3 58.1 + - - +
396A ARG* 3.3 7.3 + - - +
397A LEU* 3.0 35.9 + - + +
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Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 5.7 2.0 + - - -
69A GLN* 3.9 33.7 + - - +
72A VAL* 4.2 23.2 - - + +
390A PHE* 3.2 20.7 + - - +
391A SER* 3.3 23.4 + - - +
393A VAL* 1.3 76.9 - - - +
395A GLN* 1.3 61.5 + - + +
397A LEU* 3.6 5.8 + - - +
398A GLU* 3.2 22.7 + - - +
404A ILE* 5.1 5.4 - - + +
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Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A SER* 3.2 26.5 + - - +
392A ILE* 4.1 3.8 - - - +
394A GLU* 1.3 80.1 - - + +
396A ARG* 1.3 53.6 + - + +
397A LEU 3.0 5.4 - - - -
398A GLU* 3.4 9.6 - - + +
399A ALA* 2.6 32.9 + - - +
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Residues in contact with ARG 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLN 3.1 26.6 + - - -
204A ILE* 3.4 31.3 + - - +
205A GLY* 3.7 10.7 - - - +
392A ILE* 3.0 31.8 + - + +
393A VAL* 3.3 8.9 + - - +
395A GLN* 1.3 77.1 - - + +
397A LEU* 1.3 66.3 + - + +
399A ALA* 3.8 18.3 - - + +
400A LEU* 4.3 10.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il